how to read indexed bamfiles
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4.0 years ago
onemore100iq ▴ 20

I am trying to calculate depth by region using samtools depth command to extract depth information for specific region in chromosome_3 in a bam file.bam I indexed the bam file using samtools index bamfile.bam to bamfile.bam.bai when I typed samtools depth -r chromosome_3:10001-10010 bamfile.bam.bai
it gave erorr : could not open "bamfile.bam.bai" : Success how it could not open the bam.bai file and count it as success?

any help would be highly apprciated

next-gen • 1.9k views
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Was this bam files sorted before it was indexed?

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yes. and it worked now thanks

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You could have a look at https://github.com/brentp/mosdepth

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4.0 years ago

samtools depth -r chromosome_3:10001-10010 bamfile.bam.bai

You should point samtools to the bam file, not the index file.

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Correctly said by Chris, Input requirement for samtools depth is .bam file not .bai (indexed) file

samtools depth -r <chr:from-to> .bam

Above command should work. (Also make sure that .bam and .bai are in the same directory)

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Thanks i did as u said and it worked. Thank u so much

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Thanks Chris, it worked. La

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